[FieldTrip] unit problem when following example script: Create MNI-aligned grids in individual head-space BUG?

[Diego Lozano Soldevilla]

Hi Ingrid,

I had similar problem with MEG and  changing the units with
ft_convert_units solved the issue:

vol = ft_convert_units(vol,'cm')

If not, please file a bug with a piece of data and I'll have a look,

best,

Diego




On 11 April 2013 20:30, Ingrid Nieuwenhuis <inieuwenhuis at berkeley.edu>wrote:

> Hi all,
>
> When I follow the code according to the example matlab script "Create
> MNI-aligned grids in individual head-space" something goes all wrong with
> the units.
>
> I've followed the code (pasted below, from the wiki), but when I make the
> figure with the template head model and dipole grid, it's wrong (see
> attached ..._problem.png). The dipole grid is tiny in the bottom of the
> head model. The black area is the dipole grid, not good.
> template_grid =
>       xgrid: [1x41 double]
>       ygrid: [1x41 double]
>       zgrid: [1x41 double]
>         dim: [41 41 41]
>         pos: [68921x3 double]
>        unit: 'mm'
>      inside: [1x68910 double]
>     outside: [758 759 760 761 799 800 801 802 843 884 925]
>         cfg: [1x1 struct]
>
> It's a problem with the units, because the template grid has 'mm' in the
> unit field, but when I look in the xgrid, ygrid, zgrid and pos fields the
> numbers are clearly cm not mm. However, when I multiply my xyzgrid and pos
> field by 10, the grid is not tight (see attached ..._multiplied10.png). It
> looks like the unit problem messed up the determination of what's inside
> and outside. As you can see in the template_grid, there are only a few grid
> point outside, which is clearly not correct (maybe inside/outside was
> determined on wrong units?).
>
> So, it looks like a bug to me, or am I doing something wrong? I'm using
> the newest FT version.
>
> Thanks,
> Ingrid
>
> %%% CODE FROM WIKI %%%
> template          = ft_read_mri([cur_path_FT 'external', filesep, 'spm8',
> filesep,'templates', filesep,'T1.nii']);
> template.coordsys = 'spm'; % so that FieldTrip knows how to interpret the
> coordinate system
>
> % segment the template brain and construct a volume conduction model (i.e.
> head model): this is needed
> % for the inside/outside detection of voxels.
> cfg          = [];
> template_seg = ft_volumesegment(cfg, template);
>
> cfg          = [];
> cfg.method   = 'singleshell';
> template_vol = ft_prepare_headmodel(cfg, template_seg);
>
> % construct the dipole grid in the template brain coordinates
> % the source units are in cm
> % the negative inwardshift means an outward shift of the brain surface for
> inside/outside detection
> cfg = [];
> cfg.grid.xgrid  = -20:1:20;
> cfg.grid.ygrid  = -20:1:20;
> cfg.grid.zgrid  = -20:1:20;
> cfg.grid.unit   = 'cm';
> cfg.grid.tight  = 'yes';
> cfg.inwardshift = -1.5;
> cfg.vol        = template_vol;
> template_grid  = ft_prepare_sourcemodel(cfg);
>
> % make a figure with the template head model and dipole grid
> figure
> hold on
> ft_plot_vol(template_vol);
> ft_plot_mesh(template_grid);
>
> --
> Ingrid Nieuwenhuis PhD
> Postdoctoral Fellow
> Sleep and Neuroimaging Laboratory
> Department of Psychology
> University of California, Berkeley
> California 94720-1650
> Tolman Hall, room 5305
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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